This paper deals with a shape optimization of rubber seal of the Mobile Harbor(MH) docking system for the MH's ship-to-ship mooring with containership on the open sea. Optimizing rubber seal's geometry is a complicated problem which contains a large deformation and a contact problem at the same time. In this paper, using Full Factorial Design(FFD), combination of independent variables is obtained. The geometry is optimized to achieve minimum values of stress concentration and it is done by COMSOL Multiphysics. Optimized solution is evaluated through Response Surface Method(RSM). The optimized shape is validated by comparing the results of ABAQUS and COMSOL Multiphysics.